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Committer: Bazaar Package Importer
Author(s): Charles Plessy, David Paleino, Charles Plessy
Date: 2008-07-02 11:24:48 UTC
mfrom: (1.1.1 upstream)
Revision ID: james.westby@ubuntu.com-20080702112448-2kphz1t3xwqyi9jv

Tags: 2.0.0-1

http://bugs.debian.org/479323

[ David Paleino ]
* Updated to Standards-Version 3.8.0 (no changes needed)

[ Charles Plessy ]
* New upstream release (Closes: #479323)
  Quoting the upstream changelog:
  o Modified exonerate to work in Client:Server mode
  o Fixed --refine to work with SDP alignments
  o Disabled codegen warnings from bootstrapper during compilation
  o Added --geneticcode option for using alternative genetic codes
  o Added --splice5 and --splice3 to allow alternative splice site PSSMs
  o Fixed several bugs when scanning query sequences (eg. --forcescan query)
  o Fixed to report query on forward strand whenever possible.
  o Fixed --ryo sequence dumping with --bestn
  o Fixed a bug with missing seeds when using --annotation
  o Changed license to GPLv3
  o Added protein2dna:bestfit and protein2genome:bestfit models
    (works with exhaustive alignment only)
* Updated my email address.
* debian/control:
  - Building on glib-2.0 instead of 1.2.
  - Added a build dependancy on libreadline5-dev.
  - Augmented the long description and changed the short.
  - Added a build dependency on CDBS.
* debian/copyright made machine-readable.
* debian/rules switched to cdbs.
* debian/dirs: removed.

files added:
doc/man/man1/exonerate-server.1

doc/man/man1/fastautils.1

src/database/index.c

src/database/index.h

src/database/index.test.c

src/struct/noitree.c

src/struct/noitree.h

src/struct/noitree.test.c

src/struct/splaytree.c

src/struct/splaytree.h

src/struct/splaytree.test.c

src/util/esd2esi.c

files removed:
debian/dirs

src/program/exonerate-client.c

files modified:
COPYING

ChangeLog

Makefile.in

README

configure

configure.in

debian/changelog

debian/control

debian/copyright

debian/docs

debian/exonerate.manpages

debian/rules

doc/Makefile.in

doc/man/Makefile.in

doc/man/man1/Makefile.am

doc/man/man1/Makefile.in

doc/man/man1/exonerate.1

doc/man/man1/ipcress.1

src/Makefile.am

src/Makefile.in

src/bsdp/Makefile.am

src/bsdp/Makefile.in

src/bsdp/bsdp.c

src/bsdp/bsdp.h

src/bsdp/bsdp.test.c

src/bsdp/heuristic.c

src/bsdp/heuristic.h

src/bsdp/heuristic.test.c

src/bsdp/hpair.c

src/bsdp/hpair.h

src/bsdp/hpair.test.c

src/bsdp/sar.c

src/bsdp/sar.h

src/bsdp/sar.test.c

src/c4/Makefile.in

src/c4/alignment.c

src/c4/alignment.h

src/c4/alignment.test.c

src/c4/c4.c

src/c4/c4.h

src/c4/c4.test.c

src/c4/cgutil.c

src/c4/cgutil.h

src/c4/cgutil.test.c

src/c4/codegen.c

src/c4/codegen.h

src/c4/codegen.test.c

src/c4/layout.c

src/c4/layout.h

src/c4/layout.test.c

src/c4/opair.c

src/c4/opair.h

src/c4/opair.test.c

src/c4/optimal.c

src/c4/optimal.h

src/c4/optimal.test.c

src/c4/region.c

src/c4/region.h

src/c4/region.test.c

src/c4/subopt.c

src/c4/subopt.h

src/c4/subopt.test.c

src/c4/viterbi.c

src/c4/viterbi.h

src/c4/viterbi.test.c

src/comparison/Makefile.am

src/comparison/Makefile.in

src/comparison/comparison.c

src/comparison/comparison.h

src/comparison/comparison.test.c

src/comparison/hspset.c

src/comparison/hspset.h

src/comparison/hspset.test.c

src/comparison/match.c

src/comparison/match.h

src/comparison/match.test.c

src/comparison/pcr.c

src/comparison/pcr.h

src/comparison/pcr.test.c

src/comparison/seeder.c

src/comparison/seeder.h

src/comparison/seeder.test.c

src/comparison/wordhood.c

src/comparison/wordhood.h

src/comparison/wordhood.test.c

src/database/Makefile.am

src/database/Makefile.in

src/database/dataset.c

src/database/dataset.h

src/database/dataset.test.c

src/database/fastadb.c

src/database/fastadb.h

src/database/fastadb.test.c

src/database/fastapipe.c

src/database/fastapipe.h

src/database/fastapipe.test.c

src/general/Makefile.in

src/general/argument.c

src/general/argument.h

src/general/argument.test.c

src/general/compoundfile.c

src/general/compoundfile.h

src/general/compoundfile.test.c

src/general/lineparse.c

src/general/lineparse.h

src/general/lineparse.test.c

src/general/socket.c

src/general/socket.h

src/general/socket.test.c

src/hub/Makefile.am

src/hub/Makefile.in

src/hub/analysis.c

src/hub/analysis.h

src/hub/analysis.test.c

src/hub/bsam.c

src/hub/bsam.h

src/hub/bsam.test.c

src/hub/gam.c

src/hub/gam.h

src/hub/gam.test.c

src/model/Makefile.am

src/model/Makefile.in

src/model/affine.c

src/model/affine.h

src/model/affine.test.c

src/model/bootstrapper.c

src/model/cdna2genome.c

src/model/cdna2genome.h

src/model/cdna2genome.test.c

src/model/coding2coding.c

src/model/coding2coding.h

src/model/coding2coding.test.c

src/model/coding2genome.c

src/model/coding2genome.h

src/model/coding2genome.test.c

src/model/edit_distance.c

src/model/edit_distance.h

src/model/edit_distance.test.c

src/model/est2genome.c

src/model/est2genome.h

src/model/est2genome.test.c

src/model/frameshift.c

src/model/frameshift.h

src/model/frameshift.test.c

src/model/genome2genome.c

src/model/genome2genome.h

src/model/genome2genome.test.c

src/model/intron.c

src/model/intron.h

src/model/intron.test.c

src/model/modeltype.c

src/model/modeltype.h

src/model/modeltype.test.c

src/model/ner.c

src/model/ner.h

src/model/ner.test.c

src/model/phase.c

src/model/phase.h

src/model/phase.test.c

src/model/protein2dna.c

src/model/protein2dna.h

src/model/protein2dna.test.c

src/model/protein2genome.c

src/model/protein2genome.h

src/model/protein2genome.test.c

src/model/ungapped.c

src/model/ungapped.h

src/model/ungapped.test.c

src/program/Makefile.am

src/program/Makefile.in

src/program/exonerate-server.c

src/program/exonerate.c

src/program/ipcress.c

src/sdp/Makefile.am

src/sdp/Makefile.in

src/sdp/boundary.c

src/sdp/boundary.h

src/sdp/boundary.test.c

src/sdp/lookahead.c

src/sdp/lookahead.h

src/sdp/lookahead.test.c

src/sdp/scheduler.c

src/sdp/scheduler.h

src/sdp/scheduler.test.c

src/sdp/sdp.c

src/sdp/sdp.h

src/sdp/sdp.test.c

src/sdp/straceback.c

src/sdp/straceback.h

src/sdp/straceback.test.c

src/sequence/Makefile.am

src/sequence/Makefile.in

src/sequence/alphabet.c

src/sequence/alphabet.h

src/sequence/alphabet.test.c

src/sequence/codonsubmat.c

src/sequence/codonsubmat.h

src/sequence/codonsubmat.test.c

src/sequence/sequence.c

src/sequence/sequence.h

src/sequence/sequence.test.c

src/sequence/splice.c

src/sequence/splice.h

src/sequence/splice.test.c

src/sequence/submat.c

src/sequence/submat.h

src/sequence/submat.test.c

src/sequence/translate.c

src/sequence/translate.h

src/sequence/translate.test.c

src/struct/Makefile.am

src/struct/Makefile.in

src/struct/bitarray.c

src/struct/bitarray.h

src/struct/bitarray.test.c

src/struct/dejavu.c

src/struct/dejavu.h

src/struct/dejavu.test.c

src/struct/fsm.c

src/struct/fsm.h

src/struct/fsm.test.c

src/struct/matrix.c

src/struct/matrix.h

src/struct/matrix.test.c

src/struct/pqueue.c

src/struct/pqueue.h

src/struct/pqueue.test.c

src/struct/rangetree.c

src/struct/rangetree.h

src/struct/rangetree.test.c

src/struct/recyclebin.c

src/struct/recyclebin.h

src/struct/recyclebin.test.c

src/struct/slist.c

src/struct/slist.h

src/struct/slist.test.c

src/struct/sparsecache.c

src/struct/sparsecache.h

src/struct/sparsecache.test.c

src/struct/vfsm.c

src/struct/vfsm.h

src/struct/vfsm.test.c

src/util/Makefile.am

src/util/Makefile.in

src/util/fasta2esd.c

src/util/fastaannotatecdna.c

src/util/fastachecksum.c

src/util/fastaclean.c

src/util/fastaclip.c

src/util/fastacomposition.c

src/util/fastadiff.c

src/util/fastaexplode.c

src/util/fastafetch.c

src/util/fastahardmask.c

src/util/fastaindex.c

src/util/fastalength.c

src/util/fastanrdb.c

src/util/fastaoverlap.c

src/util/fastareformat.c

src/util/fastaremove.c

src/util/fastarevcomp.c

src/util/fastasoftmask.c

src/util/fastasort.c

src/util/fastasplit.c

src/util/fastasubseq.c

src/util/fastatranslate.c

src/util/fastavalidcds.c

test/Makefile.in

test/data/Makefile.in

test/data/cdna/Makefile.in

test/data/protein/Makefile.in

test/exonerate/Makefile.in

test/ipcress/Makefile.in

test/util/Makefile.in

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Section: science

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Priority: optional

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Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

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Uploaders: Steffen Moeller <moeller@debian.org>, Charles Plessy <charles-debian-nospam@plessy.org>

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Build-Depends: debhelper (>= 5), autotools-dev, libglib1.2-dev

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Standards-Version: 3.7.2

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XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/

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XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/exonerate

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DM-Upload-Allowed: yes

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Uploaders: Steffen Moeller <moeller@debian.org>, Charles Plessy <plessy@debian.org>

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Build-Depends: debhelper (>= 5), autotools-dev, libglib2.0-dev, libreadline5-dev, cdbs

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Standards-Version: 3.7.3

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Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/?rev=0&sc=0

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Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/exonerate/trunk/

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Homepage: http://www.ebi.ac.uk/~guy/exonerate/

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Package: exonerate

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Architecture: any

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Depends: ${shlibs:Depends}, ${misc:Depends}

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Suggests: wise

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Description: tool for comparison of long biological sequences

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Much of the functionality of the Wise dynamic programming

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suite was reimplemented in C for better efficiency.

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Exonerate is an intrinsic component of the building of

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the Ensembl genome databases, providing similarity

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scores between RNA and DNA sequences and thus determining

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splice variants and coding sequences in general.

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Description: generic tool for pairwise sequence comparison

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Exonerate allows you to align sequences using a many alignment models, using

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either exhaustive dynamic programming, or a variety of heuristics. Much of

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the functionality of the Wise dynamic programming suite was reimplemented in C

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for better efficiency. Exonerate is an intrinsic component of the building of

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the Ensembl genome databases, providing similarity scores between RNA and DNA

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sequences and thus determining splice variants and coding sequences in

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general.

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.

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An In-silico PCR Experiment Simulation System (see the ipcress man page) is

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packaged with exonerate.

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.

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This package also comes with a selection of utilities for performing

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simple manipulations quickly on fasta files beyond 2Gb

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